Scott and former Rotherham teammate Paul Hurst were appointed joint managers of Northern Premier League outfit Ilkeston Town in January 2009.
During the summer months the duo bolstered Grimsby's ranks in order for a promotion push, but were hit by a blow as previous season's top scorer and player of the year Alan Connell left to join Swindon Town.
The 2012–13 season started slowly, but by Christmas Grimsby were top of the league and leading a closely contested pack of Newport County, Wrexham and Forest Green Rovers.
On 6 January 2013 speculation about the pair's future at Blundell Park came into light when rumours circulated a potential move to Football League One side Doncaster Rovers surfaced.
Rovers who had lost manager Dean Saunders earlier that day to Wolverhampton Wanderers were rumoured to have placed Scott and Hurst on their managerial shortlist.
The Mariners, despite leading the Conference for part of the season, dropped off towards the end of the year and had to settle for 4th place, eventually losing to Newport County in the play-off semi-finals.